From 5720f2cea034f014f366886b3cb9a170a909e988 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 21 Nov 2014 14:33:08 +0000 Subject: [PATCH] JAL-1528 found and readded Colour by Chain ('rainbow color') --- help/html/features/chimera.html | 2 ++ resources/lang/Messages.properties | 2 +- src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java | 3 +-- src/jalview/gui/ChimeraViewFrame.java | 3 --- 4 files changed, 4 insertions(+), 6 deletions(-) diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index e866597..236701a 100644 --- a/help/html/features/chimera.html +++ b/help/html/features/chimera.html @@ -133,6 +133,8 @@ atoms in the displayed structures. For comprehensive details of Chimera's comman they are insertions (relative to the associated sequence in the alignment) and grey if they are N or C terminal flanks outside the region mapped to the alignment window's sequence. +
  • By Chain
    +     Uses the Chimera 'rainbow chain' command to apply a different colour to each chain.
  • Charge & Cysteine
     Highlights cysteines in yellow, anionic (Aspartic Acid or Glutamic Acid) residues in red, and cationic (Lysine or Arginine) diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 5d3667b..cabee76 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -107,7 +107,7 @@ action.change_params = Change Parameters action.apply = Apply action.apply_threshold_all_groups = Apply threshold to all groups action.apply_all_groups = Apply to all Groups -action.by_chain = By chain +action.by_chain = By Chain action.by_sequence = By Sequence action.paste_annotations = Paste Annotations action.format = Format diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 090b61d..fb03f04 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -343,8 +343,7 @@ public abstract class JalviewChimeraBinding extends public void colourByChain() { colourBySequence = false; - // this is not a valid Chimera command; is there one? Menu option hidden - evalStateCommand("select *;color chain",false); + evalStateCommand("rainbow chain", false); } public void colourByCharge() diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index cfac4ef..02865e1 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -144,9 +144,6 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable, _alignwith = new Vector(); } - // no colour by chain command in Chimera? - chainColour.setVisible(false); - // save As not yet implemented savemenu.setVisible(false); -- 1.7.10.2